PATTERNFINDER is a web-based program that searches for specific or flexible sequence patterns in a given DNA molecule. The program can import a DNA sequence file from the local machine. Alternatively, the sequence can be pasted or typed into the DNA Sequence Query window. The user may choose to analyze a part of or the whole DNA molecule. The program requires an input pattern and the maximum pattern span size. According to the user's choice of either upper strand (+, or input strand) or lower strand (-, or complementary strand) or both strands, the program then scans the DNA sequence and stores the position, sequence and strand information of matches that are found. A publication by Huang & Kowalski (2004) describes the details for using PATTERNFINDER and the associated programs (below).

BATCH PATTERNFINDER is a web-based program that searches a BATCH of DNA patterns from a given DNA molecule. Its algorithm, input and output requirments are essentially the same as PATTERNFINDER.

Two additional programs, WEB-THERMODYN and THERMOCALC , can be used in conjunction with PATTERNFINDER to analyze the the DNA helical stability of match sequences and flanking DNA. They are by default inactive and can be enabled by clicking on the corresponding checkboxes. The algorithm used to calculate the free energy from thermodynamic parameters of nearest-neighbor dinucleotides is described here.